Bad design of characters. I keep repeating this since day 1: You can't make a character be great at offense AND great at defense. That's bound to create a too big imbalance.
There's no way to fairly balance the game at this point without making the top 5 work too hard for damage and/or buffing like 2/3 of the cast.
Ideally, this is how I'd like character designs for the next MK games:
1. Great at offense, poor zoning
2. Great at zoning, poor offense
3. Great at countering zoning/offense, some footsies, bad offense/zoning
4. Great footsies, mid-range and anti-airs, some mixups, bad offense/defense
5. Superior mobility and evasion tools, low damaging combos
6. High damaging combos, little mobility and evasion
7. Average at everything.
Characters like Kung Lao, Raiden, Reptile and Kabal are great at everything (rushdown, zoning, mixup, counter and footsies). While characters like Sindel, Shang Tsung, Stryker, Sonya, Johnny Cage, Baraka and Jax are only great at one thing: zoning or rushdown. That's the problem.
We can only hope NRS learns from their mistakes.